Many institutions fail to treat applicants as online consumers and need to take steps to make their websites more like e-commerce giants such as Amazon, according to Nomensa in a report titled Enhancing the University Submission Experience.
The document claims that the increase in tuition fees has made students increasingly discerning when deciding whether or not to go on to higher education, and so a good website design is vital.
Simon Norris, chief executive of the agency, said that universities "are sadly lacking in their provision of online support to students at key points in their decision-making".
He added that institutions needed to "wake up" to the fact that deciding where to go to university was now at least partly motivated by money, and that today's students were used to viewing high-quality websites before parting with large amounts of cash.
"If universities are not presenting information to prospective students in a way that the prospective students expect, then they are setting themselves up for a very tough time commercially," he said.
Mr Norris added that certain universities stood to benefit more than others from developing their websites. Those within the Russell Group of research-intensive universities had a reputation that would "sustain them for the time being", he said.
Sheila MacNeill, assistant director of the Centre for Educational Technology and Interoperability Standards at the higher education IT consortium Jisc, agreed that there were problems across the board in the quality of university websites, often because of how they are created.
"Many look like they have been designed by committee because so many stakeholders want to get something listed on the front page," she said.
"Everyone wants their own bit of information on display. There is also a tension between what a university's marketing team feels it has to show, such as achievements in research, and what students really want to see."